(Test Bank) Fundamentals Of Biochemistry

Voet,Voet,Pratt, 4

Chemistry

Test Bank

4th Edition

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Test Bank for Fundamentals Of Biochemistry, The downloadable file consists of 447 pages, and the total size of the file is 8.6 MB. Purchase now only for highly discounted price.

Author(s): Voet, Voet, Pratt

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STUDENT COMPANION F U N D A M E N T A L S O F Biochemistry LIFE AT THE MOLECULAR LEVEL Voet Voet Pratt F O U R T H E D I T I O N Akif Uzman Jerry Johnson Joseph Eichberg William Widger Donald Voet Judith G. Voet Charlotte W. Pratt This page is intentionally left blank STUDENT COMPANION TO ACCOMPANY FUNDAMENTALS OF BIOCHEMISTRY LIFE AT THE MOLECULAR LEVEL Fourth Edition Akif Uzman University of Houston Jerry Johnson University of Houston Joseph Eichberg University of Houston William Widger University of Houston Donald Voet University of Pennsylvania Judith G. Voet Swarthmore College Charlotte W. Pratt Seattle, Washington JOHN WILEY & SONS, INC Cover Designer Madelyn Lesure Cover Illustration Norm Christiansen Cover Photos (Vitruvian Man): © Odysseus/Alamy and © Dennis Hallinan/Alamy Molecular structures clockwise from top: based on X -ray structures that were respectively determined by Richard Dickerson and Horace Drew, Caltech; Gerard Bunick, University of Tennessee; Thomas Steitz, Yale University; Alfonso Mondragón, Northwestern Univ ersity; Venki Ramakrishnan, MRC Laboratory of Molecular Biology, Cambridge, U.K.; Andrew Leslie and John Walker, MRC Laboratory of Molecular Biology, Cambridge, U.K. Founded in 1807, John Wiley & Sons, Inc. has been a valued source of knowledge and understanding for more than 200 years, helping people around the world meet their needs and fulfill their aspirations. Our company is built on a foundation of principles tha t include responsibility to the communities we serve and where we live and work. In 2008, we launched a Corporate Citizenship Initiative, a global effort to address the environmental, social, economic, and ethical challenges we face in our business. Among the issues we are addressing are carbon impact, paper specifications and procurement, ethical conduct within our business and among our vendors, and community and charitable support. For more information, please visit our website: www.wiley.com/go/citizenship . Copyright © 2012 John Wiley & Sons, Inc. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning or otherwise, except as permitted under Sections 107 or 1 08 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per -copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, websi te www.copyright.com . Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc. 111 River Street, Hoboken, NJ 07030 -5774, (201) 748-6011, fax (201) 748-6008, website http://www.wiley.com/go/permissions . To order books or for customer service, please call 1-800-CALL WILEY (225-5945). Student Companion (paperback) ISBN -13 978-1-1182 -1827 -3 Printed in the United States of America 10 9 8 7 6 5 4 3 2 1 Contents 1 Introduction to the Chemistry of Life 1 2 Water 9 3 Nucleotides, Nucleic Acids, and Genetic Information 21 4 Amino Acids 29 5 Proteins: Primary Structure 40 6 Proteins: Three -Dimensional Structure 49 7 Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies 60 8 Carbohydrates 72 9 Lipids and Biological Membranes 80 10 Membrane Transport 90 11 Enzymatic Catalysis 96 12 Enzyme Kinetics, Inhibition, and Control 108 13 Biochemical Signaling 121 14 Introd uction to Metabolism 128 15 Glucose Catabolism 137 16 Glycogen Metabolism and Gluconeogenesis 146 17 Citric Acid Cycle 154 18 Electron Transport and Oxidative Phosphorylation 160 19 Photosynthesis 169 20 Lipid Metabolism 176 21 Amino Acid Metabolism 188 22 Mammalian Fuel Metabolism: Integration and Regulation 197 23 Nucleotide Metabolism 203 24 Nucleic Acid Structure 210 25 DNA Replication, Repair, and Recombination 219 26 Transcription and RNA Processing 230 27 Protein Synthesis 238 28 Regulation of Gene Expression 247 Answers to Questions AQ-1 Solutions to Problems SP-1 Welcome to biochemistry! You are about to become acquainted with one of the most exciting scientific disciplines. The biotechnology industry, with its roots in molecular genetics, is one of the most visible manifestations of the explosion of biochemical kn owledge that has occurred during our lifetime. Drug design and novel approaches such as gene therapy rely on the fundamental knowledge of the chemistry of biological molecules, particularly proteins. Our most common diseases (e.g., diabetes and heart disease) have pleiotropic multifaceted physiological effects that are best understood in terms of biochemistry. You will soon discover that biochemistry’s impact on our lives cannot be over -emphasized. We are excited to bring you an ever -expanding understa nding of this magnificent subject! Learning biochemistry is not easy but it can be fun! Most students discover that biochemistry is a synthetic science, merging knowledge of general chemistry, organic chemistry, and biology. Hence, a more mature and creat ive kind of thinking is required to gain a deep understanding of biochemistry. In addition to a solid foundation in chemistry and biology, you will need to recognize and assimilate some general principles from other disciplines within biology, including physiology, genetics, and cell biology. In this respect, biochemistry is not all that different from nonscientific pursuits that require some degree of “lateral thinking” across disciplines. This Student Companion accompanies Fundamentals of Biochemistry Fourth Edition by Donald Voet, Judith G. Voet, and Charlotte W. Pratt. It is designed to help you master the basic concepts and exercise your analytical skills as you work your way through the textbook. Each chapter of the Student Companion is divided into four parts, beginning with a general summary reminding you of the topics covered in that chapter. This is followed by a section called Essential Concepts, which provides a n overview of the main facts and ideas that are essential for your understanding of biochemistry. This can be regarded as a set of brief notes for each chapter, alerting you to the key facts you need to commit to memory and to the concepts you need to mast er. You will soon notice that biochemical knowledge is cumulative: new concepts often rely on a solid understanding of previously presented concepts. Hence, one of the key goals of this Companion is to help you gain this understanding. The third and last s ection is the Questions. These are organized in a manner to help you gain a firm understanding of each section of a chapter. Some questions ask you to recall essential facts while others exercise your problem -solving skills. Answers to all of the questions are provided at the end of the Student Companion. However, you do yourself a great disservice by turning to them too soon. Don’t know the answer right away? Keep trying! Go back to the text to find clues for yourself. Use the answers to check yours, not to fill in a temporary void in your understanding. The Solutions to all end of chapter problems in the text can be found after the Answers to Questions. As a new addition to this edition of the Student Companion, we have added three new features to select chapters: Behind the Equations, Calculation Analogies and Play It Forward. Behind the Equations is a section that tackles key equations in Biochemistry. This section will provide insights and learning strategies for using and understanding what these equations are really telling us, and how to use them intuitively. The Calculation Analogies section will tackle key equations conceptually using simple analogies that will help students understand how to solve problems. The Play It Forward Section will take critical concepts from early chapters and integrate them into material in later chapters to help students see how the content continues to build upon itself, hopefully allowing students to synthesize Biochemistry as a discipline. “How should I study biochemistry beyond reading the textbook and working in this Companion?” is a likely question from students. The phrase, “if you don’t use it, you lose it” applies here. It is pointless to simply read your biochemistry textbook over and over. Unless you are actively engaged in working with the material, you become a passive reader. Active engagement includes using your hands to work probl ems, drawing pictures, or writing an outline or flow chart. As you read, ask yourself questions and seek answers from your text and your instructor. By doing these things, you use the material, and it becomes more efficiently transferred to your long-term memory. “How often should I study biochemistry?” is also a common question. Most instructors agree that frequent short study sessions —even daily —will pay greater dividends than a single long session once a week. Because short -term memory lasts just a few minutes, take a few minutes after every class to review your notes. Similarly, stop reading your text, and review on paper with diagrams, word charts, flow diagrams, what you just read. Talk biochemistry with anyone who will listen. Form a study group to enrich your knowledge and test your memory. All these activities will result in the transfer of knowledge from short -term memory to long - term memory. I n other words, the more you use biochemistry, the better you know it and the more fun you will have with it. One of the truly most satisfying ways to learn biochemistry is to apply its principles and findings to problems that integrate your knowledge. To this end, Dr. Kathleen Cornely has developed numerous case studies that test your analytical skills. You will find these case studies on the Fundamentals of Biochemistry 4e Student Companion Site at www.wiley.com/college/voet . They can also be found in the Fundamentals of Biochemistry 4e WileyPLUS course (www.wileyplus.com) . Topics for the case studies were chosen to cover a range of interesting areas relevant to biochemistry. The cases themselves are based on data from research reports as well as clinical studies. The prerequisites include m aterial that you are likely to be studying in biochemistry class, but occasionally include concepts from genetics and immunology on a level likely to be encountered in a first-year general biology course. The answers to the questions posed in these case studies can be obtained from your instructor. We have many people to thank for helping us get this Companion to you. First and foremost, we would like to acknowledge Associate Editor, Ms. Aly Rentrop, and Production Editor, Ms. Sandra Dumas. In addition, we would like to acknowledge Ms. Petra Recter, Associate Publisher for Physics and Chemistry at John Wiley and Sons for her support of this project. We are also indebted to Caroline Breitenberger of The Ohio State University and Laura Mitchell of St. Joseph’ s University for their much -appreciated reviews of our original draft. We would also like to thank our students at Swarthmore College, the University of Houston, and the University of Houston -Downtown for pointing out errors and ambiguities in earlier drafts of this work. It is still possible that errors persist, and so we would greatly appreciate being alerted to them. Please forward you comments to Akif Uzman (uzmana@uhd.edu ). Akif Uzman Jerry Johnson Joseph Eichberg William Widger Charlotte W. Pratt Donald Voet Judith G. Voet This page is intentionally left blank 1 Introduction to the Chemistry of Life This chapter introduces you to life at the biochemical and cellular level. It begins with a discussion of the chemical origins of life and its early evolution. This discussion continues into ideas and theories about the evolution of organisms, followed by a brief introduction to taxonomy and phylogeny viewed from a molecular perspective. The chap ter concludes with an introduction to the basic concepts of thermodynamics and its application to living systems. Biochemistry, like all other sciences, is a based on the measurement of observable phenomena. Hence, it is important to become familiar with t he conventions used to measure energy and mass. Box 1-2 presents the essential biochemical conventions that we will encounter throughout Fundamentals of Biochemistry . Essential Concepts The Origin of Life 1. Living matter consists of a relatively small number of elements, of which C, N, O, H, Ca, P, K, and S account for ~98% of the dry weight of most organisms (which are 70% water). These elements form a variety of reactive functional groups that participate in biological structure and biochemical reactions. 2. The current model for the origin of life proposes that organisms arose from the polymerization of simple organic molecules to form more complex molecules, some of which were capable of self-replication. 3. Most polymerization reactions involving the building of small organic molecules into larger more complex ones occur by the formation of water. This is called a condensation reaction. 4. A key development in the origin of life was the formation of a membrane that could separate the critic al molecules required for replication and energy capture from a potentially degradative environment. 5. Complementary surfaces of molecules and macromolecules provide a template for biological specificity (e.g., macromolecular assembly, enzyme activity, and expression and replication of the genome). 6. Modern cells can be classified as either prokaryotic or eukaryotic. Eukaryotic cells are distinguished by a variety of membrane -bounded organelles and an extensive cytoskeleton. 2 Chapter 1 Introduction to the Chemistry of Life Organismal Evolution 7. Prokaryotes show a limited range of morphologies but very diverse metabolic capabilities. 8. Phylogenetic evidence based on comparisons of ribosomal RNA genes have been used by Woese and colleagues to group all organisms into three domains: archaea, bacteria, and eukarya. 9. The evolution of sexual reproduction marks an important step of the evolution of organisms, because it allows for genetic exchanges that lead to an increase in the adaptability of a population of organisms to changing environments. 10. Eukaryotes contain several membrane -bounded structures, such as mitochondria and chloroplasts, which may be descended from ancient symbionts. 11. Archaea represent a third domain or branch of life in the three -domain system of classification. While they outwardly resemble bacteria, their genomes and the proteins encoded in them more closely resemble those of eukaryotes. 12. Biological evolution is not goal -directed, requi res some built -in sloppiness, is constrained by its past, and is ongoing. 13. Natural selection directs the evolution of species. Thermodynamics 14. The first law of thermodynamics states that energy ( U) is conserved; it can neither be created nor destroyed. 15. Enthalpy ( H) is a thermodynamic function that is a sum of the energy of the system and the product of the pressure and the volume ( PV). Since biochemical processes occur at constant pressure and have negligible changes in volume, the change of energy of the system is nearly equivalent to the change in enthalpy (U ≈ H). 16. The second law of thermodynamics states that spontaneous processe s are characterized by an increase in the entropy of the universe, that is, by the conversion of order to disorder. 17. The spontaneity of a process i s determined by its free energy change ( G = H – TS). Spontaneous reactions have G < 0 (exergonic) and nonspontaneous reactions have G > 0 (endergonic). 15. For any process at equilibrium, the rate of the forward reaction is equal to the rate of the reverse reaction, and G = 0. 18. Energy, enthalpy, entropy, and free energy are state functions; that is, they depend only on the state of the system, not its histor y. Hence, they can be measured by considering only the initial and final states of the system and ignoring the path by which the system reached its final state. Chapter 1 Introduction to the Chemistry of Life 3 19. The entropy of a solute varies with concentration; therefore, so does its free energy. The free energy change of a chemical reaction depends on the concentration of both its reacta nts and its products. 20. For the general reaction aA + bB cC + dD the free energy change is given by the following relationship: 21. The equilibrium constant of a chemical reaction is related to the standard free energy of the reaction when the reaction is at equilibrium (G = 0) as follows: G = –RT ln Keq where Keq is the equilibrium constant of the reaction: The equilibrium constant can therefore be calculated from standard free energy data and vice versa . 22. The equilibrium constant varies with temperature by the relationship: where H° and S° represent enthalpy and entropy in the standard state. A plot of Keq versus 1/T, known as a van’t Hoff plot, permits the values of H° and S° (and therefore G° at any temperature) to be determined from measurements of Keq at two (or more) temperatures. 23. The biochemical standard state is defined as follows: The temperature is 25°C, the pH is 7.0, and the pressure is 1 atm. The activities of reactants and products are taken to be the total activities of all their ionic species, except for water, which is as signed an activity of 1. [H+] is also assigned an activity of 1 at the physiologically relevant pH of 7. These conditions are different than the chemical standard state, so that the biochemical standard free energy is designated as G° and in the chemical standard state is G°. We assume that activity equals molarity for dilute solutions. 4 Chapter 1 Introduction to the Chemistry of Life 24. An isolated system cannot exchange matter or energy with its surroundings. A closed system can exchange only energy with its surroundings. A closed sys tem inevitably reaches equilibrium. Open systems exchange both matter and energy with their surroundings and therefore cannot be at equilibrium. Living organisms must exchange both matter and energy with their surroundings and are thus open systems. Living organisms tend to maintain a constant flow of matter and energy, referred to as the steady state. 25. Living systems can respond to slight perturbations from the steady state to restore the system back to the steady state. 26. The recovery of free energy from a biochemical process is never total, and some energy is lost to the surroundings as heat. Hence, while the system becomes more ordered, the surroundings experience an increase in entropy. 27. Enzymes accelerate the rate at wh ich a biochemical process reaches equilibrium. They accomplish this by interacting with reactants and products to provide a more energetically favorable pathway for the biochemical process to take place. Key Equations Be sure to know the conditions for which the following thermodynamics equations apply and be able to interpret their meaning. Chapter 1 Introduction to the Chemistry of Life 5 Calculation Analogy for Determining Gibbs Free Energy for a Chemically Defined System The change in Gibbs Free Energy ( G) is used to determine whether or not a process is spontaneous or non-spontaneous under a given set of conditions (state of a thermody namic system). For a thermodynamic system that is a chemical process such as: aA + bB cC + dD The G of this process can be determined using equation 7 (see Key Equations above): The typical student approaches a problem utilizing this equation with a ‘plug and chug’ mentality, without understanding exactly what the equation is trying to tell them. Ultimately, this equation is informing us how far a thermodynamic system is from equilibrium ( G = 0). A simple mathematical analogy can be used to demonstrate this concept and provide a visual perspective when solving problems requiring the use of this equation. Consider a number line used in mathematics: 0 Number lines are constructed with a particular reference in mind; here, the number zero. Any system located on the right -hand side of zero on the number line is characterized by a positive number and would represent a system that is non -spontaneous under t he specified conditions. Any system located on the left -hand side of zero on the number line is characterized by a negative number and would represent a system that is spontaneous under the specified conditions. Since a system at thermodynamic equilibrium has a G = 0, then any value of G  0 would represent a thermodynamic system not at equilibrium. We could use a number line to plot the position of any thermodynamic system not at equilibrium in reference to thermodynamic equilibrium ( G = 0). In doing s o, we could physically measure the distance between zero and the position of the thermodynamic system that is not at equilibrium using a ruler. You could plot the number – 30 on the number line, and this position would correspond to a thermodynamic system with a G = – 30 kJmol–1: